@@ -1,7 +1,7 @@

 Package: OncoSimulR

 Type: Package

 Title: Forward Genetic Simulation of Cancer Progresion with Epistasis 

-Version: 2.3.5

+Version: 2.3.6

 Date: 2016-06-25

 Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),

 		     email = "rdiaz02@gmail.com"),

@@ -224,10 +224,14 @@ allGenotypes_to_matrix <- function(x) {

 }

-

-magellan_stats <- function(x, max_num_genotypes = 2000,

+## Magellan_stats and Magellan_draw cannot be tested

+## routinely, as they depend on external software

+Magellan_stats <- function(x, max_num_genotypes = 2000,

                            verbose = FALSE,

-                           fl_statistics = "fl_statistics") {

+                           use_log = TRUE,

+                           short = TRUE,

+                           fl_statistics = "fl_statistics") { # nocov start

+    ## I always use 

     ## if(!is.null(x) && is.null(file))

     ##     stop("one of object or file name")

     ## if(is.null(file))

@@ -235,30 +239,77 @@ magellan_stats <- function(x, max_num_genotypes = 2000,

     fnret <- tempfile()

     if(verbose)

         cat("\n Using input file", fn, " and output file ", fnret, "\n")

+    

+    if(use_log) {

+        logarg <- "-l"

+    } else {

+        logarg <- NULL

+    }

+    if(short) {

+        shortarg <- "-s"

+    } else {

+        shortarg <- NULL

+    }

+    

     to_Magellan(x, fn, max_num_genotypes = max_num_genotypes)

-    call_M <- system(paste(fl_statistics, fn, "-s", "-o", fnret))

-    return(read.table(fnret, skip = 1, header = TRUE)[-1])

-}

+    call_M <- system2(fl_statistics, args = paste(fn, shortarg, logarg, "-o", fnret))

+    if(short) {

+        tmp <- as.vector(read.table(fnret, skip = 1, header = TRUE)[-1])

+        ## Make names more explicit, but check we have what we think we have

+        stopifnot(length(tmp) == 23)

+        stopifnot(identical(names(tmp),

+                            c("ngeno", "npeaks", "nsinks", "gamma", "gamma.", "r.s",

+                              "nchains", "nsteps", "nori", "depth", "magn", "sign",

+                              "rsign", "w.1.", "w.2.", "w.3..", "mode_w", "s.1.",

+                              "s.2.", "s.3..", "mode_s", "pairs_s", "outD_v")))

+        names(tmp) <- c("n_genotypes", "n_peaks", "n_sinks", "gamma", "gamma_star",

+                        "r/s","n_chains", "n_steps", "n_origins", "max_depth",

+                        "epist_magn", "epist_sign", "epist_rsign",

+                        "walsh_coef_1", "walsh_coef_2", "walsh_coef_3", "mode_walsh",

+                        "synerg_coef_1", "synerg_coef_2", "synerg_coef_3", "mode_synerg",

+                        "std_dev_pairs", "var_outdegree")

+    } else {

+        tmp <- readLines(fnret)

+    }

+    return(tmp)

+} # nocov end

+

+Magellan_draw <- function(x, max_num_genotypes = 2000,

+                          verbose = FALSE,

+                          args = "-f",

+                          fl_draw = "fl_draw",

+                          svg_open = "xdg-open",

+                          file_name = NULL) { # nocov start

+    ## It always works by appending the name so file_name is without the .svg

+    if(is.null(file_name)) {

+        fn <- tempfile()

+    } else {

+        fn <- file_name

+    }

+    fn_out <- paste0(fn, ".svg")

+    if(verbose)

+        cat("\n Using input file", fn, " and output file ", fn_out, "\n")

+       

+    to_Magellan(x, fn, max_num_genotypes = max_num_genotypes)

+    call_M <- system2(fl_draw, args = paste(fn, args), wait = FALSE)

+    call_view <- system2(svg_open, args = fn_out, wait = FALSE,

+                         stdout = ifelse(verbose, "", FALSE),

+                         stderr = ifelse(verbose, "", FALSE))

+    

+    invisible() 

+} # nocov end

-##

-## ## Example of Bozic issues

+## ## Example of Bozic issues in conversions of fitnes

 ## m1 <- cbind(c(0, 1), c(1, 0), c(2, 3))

-

 ## m2 <- cbind(c(1, 1), c(1, 0), c(2, 3))

-

 ## m3 <- data.frame(G = c("A, B", "A"), F = c(1, 2))

-

 ## m4 <- data.frame(G = c("A, B", "A", "WT", "B"), F = c(3, 2, 1, 4))

-

 ## m5 <- data.frame(G = c("A, B", "A", "WT", "B"), F = c(3, 2, 1, 0))

-

 ## m6 <- data.frame(G = c("A, B", "A", "WT", "B"), F = c(3, 2.5, 2, 0))

-

-

 ## And no, it makes no sense to use any of this for mutator: in mutator I

 ## directly have the multiplication factor of each gene. Which is likely

-## what people want anyway. Add it later if needed. by using a ratio

+## what people want anyway. Add it later if needed by using a ratio

 ## instead of a "-"

@@ -1,3 +1,6 @@

+Changes in version 2.3.6 (2016-06-25):

+	- improved test coverage

+	

 Changes in version 2.3.5 (2016-06-25):

 	- to_Magellan.

@@ -122,6 +122,11 @@ Ramon Diaz-Uriarte

   epistasis stats for the landscape, and several visual manipulation

   options.

+  One feature of this function that is not available in MAGELLAN is

+  showing genotype labels (i.e., annotated by gene names), which can be

+  helpful if the different genotypes mean something to you.

+

+  

   In addition to the above differences, another difference between this

   plot and those of MAGELLAN is \bold{how sinks/peaks of more than one

   genotype are dealt with}. This plot will show as sinks or peaks sets

@@ -143,7 +148,7 @@ Ramon Diaz-Uriarte

   possibility of peaks/sinks made of more than one genotype actually

   makes code much simpler.

-

+  

   Sometimes not showing the any links that involve a decrease in fitness

   can help see non-accessible pathways (in strong selection, no multiple

   mutations, etc); do this by passing, for instance, an NA for the

new file mode 100644

@@ -0,0 +1,10 @@

+test_that("Expect output", {

+    r1 <- rfitness(4)

+    expect_output(to_Magellan(r1, NULL))

+    cs <-  data.frame(parent = c(rep("Root", 3), "a", "d", "c"),

+                      child = c("a", "b", "d", "e", "c", "f"),

+                      s = 0.1,

+                      sh = -0.9,

+                      typeDep = "MN")

+    expect_output(to_Magellan(allFitnessEffects(cs), NULL))

+})

@@ -36,3 +36,63 @@ test_that("We fail with order", {

 test_that("We fail with wrong separator, :", {

     expect_error(OncoSimulR:::from_genotype_fitness(data.frame(G = "A : B", F = 1)))

 })

+

+

+test_that("Dividing fitness by wt and missing genot is 1", {

+    

+    m7 <- cbind(c(1, 1, 0), c(1, 0, 0), c(2, 3, 5))

+    expect_message(fem7 <- allFitnessEffects(genotFitness = m7),

+                   "Fitness of wildtype != 1. Dividing all fitnesses by fitness of wildtype.",

+                   fixed = TRUE)

+    expect_equivalent(evalAllGenotypes(fem7, order = FALSE, addwt = TRUE)[, 2],

+                      c(1, 3/5, 1, 2/5))

+})

+

+test_that("The WT is added if absent", {

+    m7 <- cbind(c(1, 1, 0), c(1, 0, 0), c(2, 3, 5))

+    fem7 <- allFitnessEffects(genotFitness = m7)

+    ag <- evalAllGenotypes(fem7, order = FALSE)

+    ## internal call

+    expect_equivalent(OncoSimulR:::allGenotypes_to_matrix(ag)[, 3],

+                      c(1, 3/5, 1, 2/5))

+    ## the user visible, which is via plotFitnessLandscape -> to_Fitness_Matrix

+    plot(ag)

+})

+

+

+test_that("genotFitness not combined with others", {

+

+    m7 <- cbind(c(1, 1, 0), c(1, 0, 0), c(2, 3, 5))

+    

+    expect_error(allFitnessEffects(genotFitness = m7,

+                                   noIntGenes = c(.1, .2)),

+                 "You have a non-null genotFitness.",

+                 fixed = TRUE)

+

+    expect_error(allFitnessEffects(genotFitness = m7,

+                                   epistasis = c("A" = .3,

+                                            "B" = .1,

+                                            "C" = .2)),

+                 "You have a non-null genotFitness.",

+                 fixed = TRUE)

+    

+    expect_error(allFitnessEffects(genotFitness = m7,

+                                   orderEffects = c("G > H" = 1.1)),

+                 "You have a non-null genotFitness.",

+                 fixed = TRUE)

+

+

+    p3 <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c", "f"),

+                  child = c("a", "b", "d", "e", "c", "c", "f", "f", "g", "g"),

+                  s = c(0.01, 0.02, 0.03, 0.04, 0.1, 0.1, 0.2, 0.2, 0.3, 0.3),

+                  sh = c(rep(0, 4), c(-.9, -.9), c(-.95, -.95), c(-.99, -.99)),

+                  typeDep = c(rep("--", 4), 

+                              "XMPN", "XMPN", "MN", "MN", "SM", "SM"))

+    

+    expect_error(allFitnessEffects(rT = p3, genotFitness = m7),

+                 "You have a non-null genotFitness.",

+                 fixed = TRUE)

+   

+})

+

+

@@ -210,6 +210,35 @@ test_that("eval mut genotypes", {

+test_that("eval mut genotypes, echo", {

+    fe <- allFitnessEffects(epistasis = c("a : b" = 0.3,

+                                          "b : c" = 0.5),

+                            noIntGenes = c("e" = 0.1),

+                            drvNames = c(letters[1:3]))

+    fm <- allMutatorEffects(noIntGenes = c("a" = 10,

+                                           "c" = 5))

+    expect_output(evalGenotypeMut("a, c", fm, echo = TRUE),

+                  "Mutation rate product", fixed = TRUE)

+})

+

+

+test_that("evaluating genotype and mutator, Bozic", {

+    fe <- allFitnessEffects(epistasis = c("a : b" = 0.3,

+                                          "b : c" = 0.5),

+                            drvNames = letters[1:3])

+    fm <- allMutatorEffects(noIntGenes = c("a" = 10,

+                                           "c" = 5))

+    ou <- evalAllGenotypesFitAndMut(fe, fm, order = FALSE,

+                                    model = "Bozic")

+    expect_equivalent(ou[, 2],

+                      c(1, 1, 1, 1 - .3, 1, 1 -.5, (1 -.3) * (1 - .5))

+                      )

+    expect_equivalent(ou[, 3],

+                      c(10, 1, 5, 10, 10 * 5, 5, 10 * 5)

+                      )

+})

+

+

 test_that("mut and fitness both needed when needed", {

     fe <- allFitnessEffects(epistasis = c("a : b" = 0.3,

                                           "b : c" = 0.5),

@@ -1,6 +1,10 @@

 test_that("Exercise plotting", {

     r1 <- rfitness(4)

     expect_silent(plot(r1))

+    expect_silent(plot(r1, log = TRUE))

+    expect_silent(plot(r1, log = TRUE, use_ggrepel = TRUE))

+    expect_silent(plot(r1, log = TRUE, show_labels = FALSE))

+    

     ## Specify fitness in a matrix, and plot it

     m5 <- cbind(c(0, 1, 0, 1), c(0, 0, 1, 1), c(1, 2, 3, 5.5))

@@ -12,14 +16,54 @@ test_that("Exercise plotting", {

                             noIntGenes = c("e" = 0.1))

     expect_silent(plot(evalAllGenotypes(fe, order = FALSE)))

-    

+

     ## same as

     expect_silent(plotFitnessLandscape(evalAllGenotypes(fe, order = FALSE)))

-    

+    ## more ggrepel

+    expect_silent(plot(evalAllGenotypes(fe, order = FALSE), use_ggrepel = TRUE))

+})

+

+

+test_that("to_FitnessMatrix stops as it should", {

+    x1 <- data.frame(a = 1:2, b = 1:2)

+    expect_error(OncoSimulR:::to_Fitness_Matrix(x1, 2000),

+                 "We cannot guess what you are passing",

+                 fixed = TRUE)

+    x2 <- list(a = 12, b = 13)

+    expect_error(OncoSimulR:::to_Fitness_Matrix(x2, 2000),

+                 "We cannot guess what you are passing",

+                 fixed = TRUE)

 })

+test_that("to_FitnessMatrix can deal with df", {

+    m4 <- data.frame(G = c("A, B", "A", "WT", "B"),

+                     Fitness = c(3, 2, 1, 4))

+    expect_message(OncoSimulR:::to_Fitness_Matrix(m4, 2000),

+                   "Column names of object", fixed = TRUE)

+    m5 <- data.frame(G = c("A, B", "B"),

+                     Fitness = c(3, 2))

+    expect_message(OncoSimulR:::to_Fitness_Matrix(m5, 2000),

+                   "Column names of object", fixed = TRUE)

+    x1 <- data.frame(a = c("A, B"), Fitness = 2)

+    expect_message(OncoSimulR:::to_Fitness_Matrix(x1, 2000),

+                   "Column names of object", fixed = TRUE)

+    x2 <- data.frame(a = c("A, B", "B"), Fitness = c(2, 3))

+    expect_message(OncoSimulR:::to_Fitness_Matrix(x2, 2000),

+                   "Column names of object", fixed = TRUE)

+    x3 <- data.frame(a = c("A, B", "C"), Fitness = c(2, 3))

+    expect_message(OncoSimulR:::to_Fitness_Matrix(x3, 2000),

+                   "Column names of object", fixed = TRUE)

+    ## Now, the user code

+    expect_message(plotFitnessLandscape(x1))

+    expect_message(plotFitnessLandscape(x2))

+    expect_message(plotFitnessLandscape(x3))

+    expect_message(plotFitnessLandscape(m5))

+    expect_message(plotFitnessLandscape(m4))

+})

+

+

 test_that("internal peak valley functions", {

     x <- matrix(NA, 14, 14)

@@ -387,5 +387,22 @@ test_that("exercising sampling code, customSize", {

+test_that("exercising sampling code, customSize", {

+    cs <-  data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),

+                                child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),

+                      s = 0.1,

+                                sh = -0.9,

+                      typeDep = "MN")

+    cbn1 <- allFitnessEffects(cs, drvNames = c("a", "b", "c", "d", "e", "g"))

+    o1 <- oncoSimulIndiv(cbn1, detectionSize = 1e8,

+                         onlyCancer = TRUE,

+                         detectionDrivers = 1,

+                         max.num.tries = 5000,

+                         sampleEvery = 0.03,

+                         keepEvery = 1000000)

+    expect_message(samplePop(o1, timeSample = "unif"),

+                   "Only one sampled time period with mutants", fixed = TRUE)

+})

+

 cat(paste("\n Ending samplePop tests", date(), "\n"))

@@ -1,15 +1,15 @@

 \usepackage[%

-		shash={a8daef6},

-		lhash={a8daef6cae6f3c218599ea59264b950e95040f54},

-		authname={Ramon Diaz-Uriarte},

-		authemail={rdiaz02@users.noreply.github.com},

-		authsdate={2016-06-24},

-		authidate={2016-06-24 10:14:31 +0200},

-		authudate={1466756071},

-		commname={Ramon Diaz-Uriarte},

-		commemail={rdiaz02@users.noreply.github.com},

-		commsdate={2016-06-24},

-		commidate={2016-06-24 10:14:31 +0200},

-		commudate={1466756071},

-		refnames={ (HEAD, origin/master, origin/HEAD)}

+		shash={3f0ca61},

+		lhash={3f0ca612b9bf91cbc9e99fcaa84a03de2fb1446d},

+		authname={ramon diaz-uriarte (at Bufo)},

+		authemail={rdiaz02@gmail.com},

+		authsdate={2016-06-25},

+		authidate={2016-06-25 14:02:01 +0200},

+		authudate={1466856121},

+		commname={ramon diaz-uriarte (at Bufo)},

+		commemail={rdiaz02@gmail.com},

+		commsdate={2016-06-25},

+		commidate={2016-06-25 14:02:01 +0200},

+		commudate={1466856121},

+		refnames={ (HEAD -> master, origin/master, origin/HEAD)}

 	]{gitsetinfo}

\ No newline at end of file